INVESTIGATING THE EFFECTS OF IONIC LIQUIDS ON DNA GQUADRUPLEX AND PROTEIN STRUCTURE USING MOLECULAR DYNAMICS SIMULATIONS

Nucleic acids and proteins have huge implications in biomedicine and bioengineering, however their storage instability limits their applicability and current storage protocols are expensive and globally-inaccessible. Finding an alternative biocompatible media to store nucleic acids and proteins would reduce costs and increase their applicability. Ionic liquids (ILs) are molten salt compounds that have been shown to modulate the stability and activity of nucleic acids and proteins. In this thesis, molecular modeling studies of DNA/RNA and protein structure in ILs will be discussed (Chapter 1) and this method will be used to study the IL effects on the structure on the Pu22 c-MYC DNA G-quadruplex (Chapter 2) and the azurin protein (Chapter 3). ILs have been observed to stabilize/destabilize DNA G-quadruplexes linked to cancer oncogene expression, however the structural effects of imidazolium-based ILs on G-quadruplexes remain unknown. Bioengineering of azurin is attractive for soil bioremediation, thus understanding the structural changes induced by TMG amino acid-based ILs will mediate future IL design for enhancing azurin\u27s activity. In Chapter 2, molecular dynamics (MD) simulations will elucidate the stabilizing mechanism of four imidazolium-based ILs of increasing hydrophobicity to Pu22, using the G-quadruplex stabilizer TMPyP4 as a molecular probe. In Chapter 3, conventional and replica-exchange MD simulations will provide insight into the enthalpic and entropic change induced by two TMG-AA based ILs on the folded and unfolded azurin conformations

Near-Neutral Balanced Selection Theory (NNBST): Implication on the molecular evolution of SARS-CoV-2 and Zika virus

Virus pandemics have significantly impacted human welfare and development. Understanding the true molecular evolution of viruses is critical for preventing future pandemics and developing the next-generation drugs and vaccines. Unfortunately, viruses exhibiting constant genomic substitution rates (GSRs) despite increasing vaccinations and human infections (SARS-CoV-2) and viruses under seemingly extreme conservation (ZIKV) paints a confusing picture of viral evolution, and the main evolutionary theories (Selectionist Theory, Kimura’s Neutral Theory) cannot explain their molecular evolution. Here, we developed a first-principle model, c/u, to characterize reproductive fitness changes in viruses based on variations in the nucleotide/codon mutation rate (c) with respect to the global genomic mutation rate (u). c/u is nucleotide-centric, since phenotypic changes in proteins are reflected by genotypic changes in genes. c/u can assign selection types to coding regions (virus function) and non-coding untranslated regions (UTRs, virus gene regulation). Additionally, c/u can handle conserved sites (c/u=0) and sites with few mutations under false positive selection (c/u\u3c\u3c\u3e\u3e1). The constant GSRs of SARS-CoV-2 and ZIKV are seemingly under effective neutral selection (c/u=1), indicating no advantageous/disadvantageous fitness change. Yet, the L-shaped probability distribution of c/u for a NT site indicates high sequence conservation, with higher c/u values being increasingly uncommon. Varying nucleotide and segment substitution rates were observed in both viruses, indicating a mixture of advantageous selection (c/u\u3e1) and purifying selection (c/

Інноваційні чинники макроекономічної динаміки

Проаналізовано взаємозв’язок економічних циклів та інновацій. Запропоновано концептуальну схему впливу інновацій на економічне зростання. Обґрунтовано напрями активізації інноваційного чинника задля виходу національних господарств на траєкторію економічного зростання.Проведен анализ взаимосвязи экономических циклов и инноваций. Предложена концептуальная схема влияния инноваций на экономический рост. Обоснованы направления активизации инновационного фактора с целью выхода национальных хозяйств на траекторию экономического роста.The interconnections between economic cycles and innovation are analyzed. Conceptual framework for the influence of innovation on economic growth is proposed. Areas of enhanced innovation factor and output of national economies on the path of economic growth are grounded

Alien Registration- Morrill, Germaine J. (Limerick, York County)

https://digitalmaine.com/alien_docs/3237/thumbnail.jp

Monte Carlo Hamiltonian of lattice gauge theory

We discuss how the concept of the Monte Carlo Hamiltonian can be applied to lattice gauge theories.Comment: "Non-Perturbative Quantum Field Theory: Lattice and Beyond", Guangzhou, China 200

Extinction and dust/gas ratio in LMC molecular clouds

Aims. The goal of this paper is to measure the dust content and distribution in the Large Magellanic Cloud (LMC) by comparing extinction maps produced in the near-infrared wavelengths and the spatial distribution of the neutral and molecular gas, as traced by Hi and CO observations. Methods. In order to derive an extinction map of the LMC, we have developed a new method to measure the color excess of dark clouds, using the 2MASS all-sky survey. Classical methods to measure the color excess (including the NICE method) tend to underestimate the true color excess if the clouds are significantly contaminated by unreddened foreground stars, as is the case in the LMC. We propose a new method that uses the color of the X percentile reddest stars and which is robust against such contamination. Using this method, it is possible to infer the positions of dark clouds with respect to the star distribution by comparing the observed color excess as a function of the percentile used and that predicted by a model. Results. On the basis of the resulting extinction map, we perform a correlation analysis for a set of dark molecular clouds. Assuming similar infrared absorption properties for the dust in the neutral and molecular phases, we derive the absorption-to-column density ratio AV/NH and the CO-to-H2 conversion factor X_(CO). We show that AV/NH increases from the outskirts of the LMC towards the 30 Dor star-forming region. This can be explained either by a systematic increase of the dust abundance, or by the presence of an additional gas component not traced by Hi or CO, but strongly correlated to the Hi distribution. If dust abundance is allowed to vary, the derived X_(CO) factors for the selected regions are several times lower than those derived from a virial analysis of the CO data. This could indicate that molecular clouds in the LMC are not gravitationally bound, or that they are bounded by substantial external pressure. However, the X_(CO) values derived from absorption can be reconciled with the virial results assuming a constant value for the dust abundance and the existence of an additional, unseen gas component. These results are in agreement with those derived for the LMC from diffuse far-infrared emission

Brucite - Industrial Mineral with a Future

Brucite, Mg(OH)2, is an uncommon mineral primarily known to mineral collectors, and to specialists studying contact metamorphic and ultramafic rocks. It is an environmentally friendly flame-retardant and is in commercial demand; it also represents a potential ore source for the metal, magnesium, which is itself in great demand. The present brucite market for flame-retardants is less than 50 000 tonnes annually, but it is increasing exponentially. Brucite has the advantage of not containing CO2; hence none is released during calcination, a positive feature in today’s society concerned with climate change. This review paper summarises the topic for scientists studying the thermodynamic properties of brucite, geologists studying its contact meta-morphic characteristics, exploration geologists and potential end-users. Given the demand for the mineral and metal, high-grade brucite deposits may become hot exploration targets within the next few years. SOMMAIRE La brucite, Mg(OH)2, est un minéral plutôt rare connu surtout des collectionneurs de minéraux et des spécialistes du métamorphisme de contact et des roches ultramafiques. La brucite est un matériau ignifuge écologique qui est en demande commercialement; il représente aussi une source potentielle de magnésium métallique, pour lequel existe une forte demande. La demande actuelle de brucite comme matériau ignifuge est de moins de 50 000 tonnes annuellement, mais elle croît exponentiellement. La brucite a l'avantage de ne pas contenir de CO2; et donc, aucun CO2 n'est produit lors de sa calcination, caractéristique très appréciée en ces temps d'inquiétudes en regard des changements climatiques. Notre article de synthèse présente un résumé de la question à l'intention des scientifiques intéressés par les propriétés thermodynamique de la brucite, aux géologues intéressés par ses caractéristiques de minéral de métamorphisme de contact, ainsi qu'aux géologues en général et aux utilisateurs. Étant donné la demande de brucite comme minéral et comme source de métal, les bons gisements de brucite pourraient constituer des cibles d'exploration dans un avenir rapproché

Economic Geology Models 5. Specialty, Critical, Battery, Magnet and Photovoltaic Materials: Market Facts, Projections and Implications for Exploration and Development

Many exploration companies are now focusing on specialty materials that are associated with so-called ‘green technology’. These include ‘battery materials’, ‘magnet materials’ and ‘photovoltaic materials’, and many such commodities are also broadly labelled as ‘critical materials’ because they are seen as vital for industrial development, societal needs or national security. The definitions used for such materials are not always consistent among jurisdictions or across industry, and this paper attempts to clarify the criteria and address some common misconceptions. The distinction between major minerals (e.g. base metals) and ‘specialty materials’ (i.e. those mined or produced in much smaller amounts) is particularly important.   The markets for many specialty materials are growing faster than those for traditional ferrous, precious and base metals and they are often portrayed as excellent long-term investment opportunities. However, the small market bases for specialty materials and considerable uncertainty around growth projections (especially related to material substitutions and rapid technological change) need to be taken into consideration for objective assessment of the development potential of any proposed project, establishment of new supply chains by major corporations, and responsible decision-making (mineral policy) by government. In the short-term, projects aimed at specialty materials (materials with a small market base) cannot benefit from economy of scale, and their development hinges on commercially proven metallurgical processes, unless they are supported by governments or end-users.   Several specialty metals (e.g. germanium, indium, cadmium, and cobalt) are commonly obtained as by-product of base metal extraction. In such cases, systematic testing of base metal ores for their specialty metal content may justify the addition of relevant recovery circuits to existing smelters. If positive results are obtained, the need for targeting new sources of such specialty metals as primary exploration targets may be reduced or eliminated.   Where market conditions permit and concerns about the future availability of materials seem reliable, grass-roots exploration for specialty materials is warranted, and pre-competitive government involvement may be justified to promote such development efforts.De nombreuses sociétés d'exploration se concentrent désormais sur les matériaux spécialisés associés à ce que l'on appelle la « technologie verte ». Ceux-ci incluent les « matériaux pour batterie », les « matériaux magnétiques » et les « matériaux photovoltaïques », et de nombreux produits de ce type sont aussi largement étiquetés comme « matériaux critiques » car ils sont considérés comme vitaux pour le développement industriel, les besoins sociétaux ou la sécurité nationale. Les définitions utilisées pour ces matériaux ne sont pas toujours cohérentes entre les juridictions ou dans l'industrie, et ce document tente de clarifier les critères et de répondre à certaines idées fausses courantes. La distinction entre les principaux minéraux (par exemple les métaux de base) et les « matériaux spécialisés » (c'est-à-dire ceux extraits ou produits en quantités beaucoup plus faibles) est particulièrement importante.  Les marchés de nombreux matériaux spécialisés croissent plus rapidement que ceux des métaux ferreux, précieux et de base traditionnels et ils sont souvent présentés comme d'excellentes opportunités d'investissement à long terme. Cependant, le marché restreint des matériaux spécialisés et l'incertitude considérable entourant les projections de croissance (en particulier liées aux substitutions de matériaux et aux changements technologiques rapides) doivent être pris en considération pour une évaluation objective du potentiel de développement de tout projet proposé, l'établissement de nouvelles chaînes d'approvisionnement par les grandes entreprises et une prise de décisions responsable par le gouvernement (politique minière). À court terme, les projets visant des matériaux spécialisés (matériaux ayant un marché restreint) ne peuvent pas bénéficier d'économies d'échelle et leur développement repose sur des procédés métallurgiques commercialement éprouvés, à moins qu'ils ne soient soutenus par les gouvernements ou les utilisateurs finaux.  Plusieurs métaux spécialisés (par exemple le germanium, l'indium, le cadmium et le cobalt) sont couramment obtenus comme sous-produits de l'extraction des métaux de base. Dans de tels cas, l'analyse systématique des minerais de métaux de base pour leur teneur en métaux spécialisés peut justifier l'ajout de circuits de récupération adéquats aux fonderies existantes. Si des résultats positifs sont obtenus, la nécessité de cibler de nouvelles sources de ces métaux spécialisés en tant que cibles d'exploration primaires peut être réduite ou éliminée.  Lorsque les conditions du marché le permettent et que les craintes quant à la disponibilité future des matériaux semblent fiables, l'exploration primaire de matériaux spécialisés est justifiée, et la participation préconcurrentielle du gouvernement peut être justifiée pour promouvoir de tels efforts de développement.

Measure of the path integral in lattice gauge theory

We show how to construct the measure of the path integral in lattice gauge theory. This measure contains a factor beyond the standard Haar measure. Such factor becomes relevant for the calculation of a single transition amplitude (in contrast to the calculation of ratios of amplitudes). Single amplitudes are required for computation of the partition function and the free energy. For U(1) lattice gauge theory, we present a numerical simulation of the transition amplitude comparing the path integral with the evolution in terms of the Hamiltonian, showing good agreement.Comment: 5 pages, 2 figure